Add reconstruction action

cockpit

@@ -56,6 +56,10 @@ def have_flats(path):
             glob.glob(os.path.join(small, '*.tif')))
 
 
+def have_params(path):
+    return os.path.exists(os.path.join(path, 'params.json'))
+
+
 class Configuration(object):
 
     def __init__(self, source, destination):
@@ -219,6 +223,7 @@ class StateMachine(object):
     FLATCORRECT = 4
     OPTIMIZE = 5
     QUICK_OPTIMIZE = 6
+    RECONSTRUCT = 7
 
     def __init__(self):
         self.current = StateMachine.START
@@ -231,6 +236,7 @@ class StateMachine(object):
             StateMachine.SYNC: collections.OrderedDict(),
             StateMachine.OPTIMIZE: collections.OrderedDict(),
             StateMachine.QUICK_OPTIMIZE: collections.OrderedDict(),
+            StateMachine.RECONSTRUCT: collections.OrderedDict(),
         }
 
     def add_action(self, from_state, action):
@@ -343,6 +349,38 @@ class Application(object):
 
         return self.run_command(cmd)
 
+    def on_reconstruct(self):
+        self.log.highlight("Reconstructing ...")
+
+        with open(os.path.join(self.prefix, 'params.json')) as f:
+            info = self.read_info()
+            opt = json.load(f)
+
+            lamino_angle = opt['lamino-angle']['value']
+            axis = opt['x-center']['value']
+
+            x_region = 960
+            y_region = 960
+
+            cmd = ('tofu lamino --verbose'
+                   ' --projections {prefix}/fc'
+                   ' --x-region="-{x_region},{x_region},1"'
+                   ' --y-region="-{y_region},{y_region},1"'
+                   ' --lamino-angle {lamino_angle}'
+                   ' --axis {x_axis},{y_axis}'
+                   ' --overall-angle -360'
+                   ' --pixel-size {pixel_size}e-6'
+                   ' --roll-angle 0'
+                   ' --slices-per-device 600'
+                   ' --output {prefix}/Slices'
+                   .format(pixel_size=info['PixelSize'],
+                           x_region=x_region, y_region=y_region,
+                           lamino_angle=lamino_angle,
+                           x_axis=axis, y_axis=float(info['Dim_2']) / 2,
+                           prefix=self.prefix))
+
+        return self.run_command(cmd)
+
     def on_quit(self):
         self.running = False
         return True
@@ -435,6 +473,7 @@ class Application(object):
         clean = Action('c', 'Clean', self.on_clean, machine.CLEAN)
         quick_optimize = Action('q', 'Quick', self.on_quick_optimize, machine.QUICK_OPTIMIZE)
         optimize = Action('o', 'Optimize', self.on_optimize, machine.OPTIMIZE)
+        reconstruct = Action('r', 'Reconstruct', self.on_reconstruct, machine.RECONSTRUCT)
 
         machine.add_action(machine.START, sync)
         machine.add_action(machine.START, quick_optimize)
@@ -443,16 +482,20 @@ class Application(object):
 
         machine.add_action(machine.SYNC, quit)
 
-        machine.add_action(machine.QUICK_OPTIMIZE, sync)
+        machine.add_action(machine.QUICK_OPTIMIZE, reconstruct)
         machine.add_action(machine.QUICK_OPTIMIZE, optimize)
         machine.add_action(machine.QUICK_OPTIMIZE, quit)
 
-        machine.add_action(machine.OPTIMIZE, sync)
+        machine.add_action(machine.OPTIMIZE, reconstruct)
+        machine.add_action(machine.OPTIMIZE, quick_optimize)
         machine.add_action(machine.OPTIMIZE, quit)
 
         machine.add_action(machine.CLEAN, sync)
         machine.add_action(machine.CLEAN, quit)
 
+        if have_params(self.config.destination):
+            machine.add_action(machine.START, reconstruct)
+
         if not have_flats(self.config.destination):
             flatcorrect = Action('f', 'Flat correct', self.on_flat_correct, machine.FLATCORRECT)
             machine.add_action(machine.START, flatcorrect)